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In 1776, the New York Provincial Congress appointed an Auditor-General to settle the public accounts. After his resignation, the Council of Appointment appointed an Auditor to succeed. In 1797, the office of the State Comptroller was created by the State Legislature to succeed the State Auditor. The Comptroller was appointed by the Council of Appointment to a one-year term, and could be re-appointed without term limit. In 1800, the Legislature reduced the salary of the Comptroller from $3,000 to $2,500, and Samuel Jones declined to be re-appointed.

Under the Constitution of 1821, the Comptroller was elected by joint ballot of the New York State Legislature to a three-year term. Under the Constitution of 1846, the office became elective by general election, and the Comptroller was elected with the other state cabinet officers in odd years to a two-year term, serving in the second year of the governor in office and the first year of the succeeding governor. The comptroller was elected in 1895 to a three-year term, and subsequently the state officers were elected in even years and served a two-year term concurrently with the governor. In 1926, the responsibilities of the New York State Treasurer were transferred to the Comptroller as the head of the Department of Audit and Control. Since 1938, the comptroller has been elected to a four-year term, like the governor.